On a second thought, instead of changing the player to fit the level, you can actually do the opposite and make a story about it!
Something like "You have boarded the enemy ship and need to wipe them out/get to the reactor chamber and blow it up/etc." - This way the player is an invader, and it makes sense that they look foreign.
This allows for several differently themed levels each in different color and with unique enemies. Also, maybe different objectives (kill all enemies, get to the point, protect an npc ally while they are setting up some mechanism, etc.)
But if you go this route, the explanation should probably be in the game itself, not in the description on the game page (add cutscenes with mission debriefs before each level, explaining why the player is there and what they are required to do, or something similar)
It can make the game even more interesting, but it also requires a lot of work (I don't know how much you want to expand this project).